From 56bd759df1d0c750a065b8c845e93d5dfa6b549d Mon Sep 17 00:00:00 2001 From: "Robin H. Johnson" Date: Sat, 8 Aug 2015 13:49:04 -0700 Subject: proj/gentoo: Initial commit MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit This commit represents a new era for Gentoo: Storing the gentoo-x86 tree in Git, as converted from CVS. This commit is the start of the NEW history. Any historical data is intended to be grafted onto this point. Creation process: 1. Take final CVS checkout snapshot 2. Remove ALL ChangeLog* files 3. Transform all Manifests to thin 4. Remove empty Manifests 5. Convert all stale $Header$/$Id$ CVS keywords to non-expanded Git $Id$ 5.1. Do not touch files with -kb/-ko keyword flags. Signed-off-by: Robin H. Johnson X-Thanks: Alec Warner - did the GSoC 2006 migration tests X-Thanks: Robin H. Johnson - infra guy, herding this project X-Thanks: Nguyen Thai Ngoc Duy - Former Gentoo developer, wrote Git features for the migration X-Thanks: Brian Harring - wrote much python to improve cvs2svn X-Thanks: Rich Freeman - validation scripts X-Thanks: Patrick Lauer - Gentoo dev, running new 2014 work in migration X-Thanks: Michał Górny - scripts, QA, nagging X-Thanks: All of other Gentoo developers - many ideas and lots of paint on the bikeshed --- sci-chemistry/phaser/Manifest | 1 + .../phaser/files/phaser-2.1.4-chmod.patch | 13 +++ sci-chemistry/phaser/metadata.xml | 9 ++ sci-chemistry/phaser/phaser-2.1.4.ebuild | 115 +++++++++++++++++++++ 4 files changed, 138 insertions(+) create mode 100644 sci-chemistry/phaser/Manifest create mode 100644 sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch create mode 100644 sci-chemistry/phaser/metadata.xml create mode 100644 sci-chemistry/phaser/phaser-2.1.4.ebuild (limited to 'sci-chemistry/phaser') diff --git a/sci-chemistry/phaser/Manifest b/sci-chemistry/phaser/Manifest new file mode 100644 index 000000000000..33872db5dc96 --- /dev/null +++ b/sci-chemistry/phaser/Manifest @@ -0,0 +1 @@ +DIST ccp4-6.1.13-phaser-cctbx-src.tar.gz 22021353 SHA256 e6c4365cb34da5ce2dd5f1e74b8927258064016194446163418c8a3139a4b804 diff --git a/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch new file mode 100644 index 000000000000..5311cb332785 --- /dev/null +++ b/sci-chemistry/phaser/files/phaser-2.1.4-chmod.patch @@ -0,0 +1,13 @@ +diff --git a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py +index 3b1bd3a..8939a74 100755 +--- a/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py ++++ b/lib/cctbx/cctbx_sources/libtbx/libtbx/config.py +@@ -802,8 +802,6 @@ class environment: + else: + action = self.write_bin_sh_dispatcher + ext = "" +- try: os.chmod(source_file, 0755) +- except OSError: pass + target_file_ext = target_file + ext + remove_or_rename(target_file_ext) + try: action(source_file, target_file_ext) diff --git a/sci-chemistry/phaser/metadata.xml b/sci-chemistry/phaser/metadata.xml new file mode 100644 index 000000000000..6b4826474daa --- /dev/null +++ b/sci-chemistry/phaser/metadata.xml @@ -0,0 +1,9 @@ + + + + sci-chemistry + + jlec@gentoo.org + ccp4 maintainer + + diff --git a/sci-chemistry/phaser/phaser-2.1.4.ebuild b/sci-chemistry/phaser/phaser-2.1.4.ebuild new file mode 100644 index 000000000000..86fa57f52603 --- /dev/null +++ b/sci-chemistry/phaser/phaser-2.1.4.ebuild @@ -0,0 +1,115 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=5 + +PYTHON_COMPAT=( python2_7 ) + +inherit eutils flag-o-matic python-single-r1 toolchain-funcs + +CCP4VER="6.1.13" + +DESCRIPTION="A program for phasing macromolecular crystal structures" +HOMEPAGE="http://www-structmed.cimr.cam.ac.uk/phaser" +SRC_URI="ftp://ftp.ccp4.ac.uk/ccp4/${CCP4VER}/ccp4-${CCP4VER}-${PN}-cctbx-src.tar.gz" + +LICENSE="|| ( phaser phaser-com ccp4 )" +SLOT="0" +#KEYWORDS="~amd64 ~x86" +KEYWORDS="" +IUSE="openmp" + +RDEPEND="" +DEPEND="${RDEPEND} + app-shells/tcsh" + +S="${WORKDIR}"/ccp4-${CCP4VER} + +src_prepare() { + epatch \ + "${FILESDIR}"/phaser-2.1.4-chmod.patch \ + "${FILESDIR}"/phaser-2.1.4-ldflags.patch + + use openmp && append-flags -fopenmp + + for i in ${CXXFLAGS}; do + OPTS="${OPTS} \"${i}\"," + done + + OPTS=${OPTS%,} + + sed -i \ + -e "s:opts = \[.*\]$:opts = \[${OPTS}\]:g" \ + "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die + + for i in ${LDFLAGS}; do + OPTSLD="${OPTSLD} \"${i}\"," + done + + sed -i \ + -e "s:env_etc.shlinkflags .* \"-shared\":env_etc.shlinkflags = \[ ${OPTSLD} \"-shared\"\]:g" \ + -e "s:\[\"-static:\[${OPTSLD} \"-static:g" \ + "${S}"/lib/cctbx/cctbx_sources/libtbx/SConscript || die + +} + +src_configure() { + local compiler + local mtype + local mversion + local nproc + + # Valid compilers are win32_cl, sunos_CC, unix_gcc, unix_ecc, + # unix_icc, unix_icpc, tru64_cxx, hp_ux11_aCC, irix_CC, + # darwin_c++, darwin_gcc. The build systems seems to prepend + # unix_ all by itself. Can this be derived from $(tc-getCC)? + compiler=$(expr match "$(tc-getCC)" '.*\([a-z]cc\)') + + # Breaks cross compilation. + mtype=$(src/${PN}/bin/machine_type) + mversion=$(src/${PN}/bin/machine_version) + + einfo "Creating build directory" + mkdir build + cd build + ln -sf "${S}/lib/cctbx/cctbx_sources/scons" scons + ln -sf "${S}/lib/cctbx/cctbx_sources/libtbx" libtbx + + einfo "Configuring phaser components" + $(PYTHON) "libtbx/configure.py" \ + --build=release \ + --compiler=${compiler} \ + --repository="${S}"/src/${PN}/source \ + --repository="${S}"/lib/cctbx/cctbx_sources \ + --static_libraries \ + ccp4io="${S}" \ + mmtbx \ + phaser || die "configure.py failed" +} + +src_compile() { + nproc=`echo "-j1 ${MAKEOPTS}" \ + | sed -e "s/.*\(-j\s*\|--jobs=\)\([0-9]\+\).*/\2/"` + + cd build + einfo "Setting up build environment" + source setpaths.sh + + einfo "Compiling phaser components" + libtbx.scons -j ${nproc} || die "libtbx.scons failed" +} + +src_install() { + dobin build/exe/phaser || die + + cat >> "${T}"/53${PN} <<- EOF + PHASER="${EPREFIX}/usr/bin" + PHASER_ENVIRONMENT="1" + PHASER_MTYPE="${mtype}" + PHASER_MVERSION="${mversion}" + PHASER_VERSION="${PV}" + EOF + + doenvd "${T}"/53${PN} || die +} -- cgit v1.2.3-65-gdbad